Meneco

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Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks


Please log in to perform a job with this app.


You must provide four SBML Files to upload and assign their roles in the Parameters:

  • --seeds file1.sbml
  • --targets file2.sbml
  • --repairnet file3.sbml
  • --draftnet file4.sbml

For have the list of all targets you can add in the Parameters:

  • --enumerate

In input :

draft.sbml

    

repair.sbml

    

seeds.sbml

    

targets.sbml

    


In output :

allgo.log
--seeds seeds.sbml --draftnet draft.sbml --repairnet repair.sbml --targets targets.sbml --enumerate
Reading draft network from draft.sbml
Reading seeds from seeds.sbml
Reading targets from targets.sbml

Checking draftnet for unproducible targets
31 unproducible targets:
M_cl_c
M_pe161_p
M_10fthf_c
M_mobd_c
M_2ohph_c
M_pydx5p_c
M_cys_DASH_L_c
M_pe160_c
M_udcpdp_c
M_dctp_c
M_coa_c
M_pe160_p
M_fad_c
M_sheme_c
M_met_DASH_L_c
M_utp_c
M_so4_c
M_fe3_c
M_pe161_c
M_pheme_c
M_datp_c
M_cu2_c
M_mlthf_c
M_adp_c
M_nad_c
M_gtp_c
M_nadp_c
M_thf_c
M_amet_c
M_dgtp_c
M_ribflv_c

Reading repair network from repair.sbml
done

Checking draftnet + repairnet for unproducible targets
  still 29 unproducible targets:
M_10fthf_c
M_mobd_c
M_2ohph_c
M_pydx5p_c
M_cys_DASH_L_c
M_pe160_c
M_udcpdp_c
M_dctp_c
M_coa_c
M_pe160_p
M_fad_c
M_sheme_c
M_met_DASH_L_c
M_utp_c
M_thf_c
M_so4_c
M_fe3_c
M_pe161_c
M_pheme_c
M_datp_c
M_mlthf_c
M_adp_c
M_nad_c
M_gtp_c
M_nadp_c
M_pe161_p
M_amet_c
M_dgtp_c
M_ribflv_c

 2 targets to reconstruct:
M_cu2_c
M_cl_c

Computing essential reactions for M_cu2_c
 1 essential reactions found:
R_CU2tpp

Computing essential reactions for M_cl_c
 1 essential reactions found:
R_CLt3_2pp

Overall 2 essential reactions found.
R_CLt3_2pp
R_CU2tpp

Adding essential reactions to network.

Computing one minimal completion to produce all targets
R_CLt3_2pp
R_CU2tpp

Computing common reactions in all completion with size 2
R_CLt3_2pp
R_CU2tpp

Computing union of reactions from all completion with size 2
R_CLt3_2pp
R_CU2tpp

Computing all completions with size 2
Completion 1: 
R_CLt3_2pp
R_CU2tpp
The workdir contains:
total 5336
-rw-r--r-- 1 500 500    1621 Mar 10 10:31 allgo.log
-rw-r--r-- 1 500 500 1099262 Mar 10 10:30 draft.sbml
-rw------- 1 500 500 1022934 Mar 10 10:31 meneco_0eptfrul.lp
-rw-r--r-- 1 500 500 3280456 Mar 10 10:30 repair.sbml
-rw-r--r-- 1 500 500   45485 Mar 10 10:30 seeds.sbml
-rw-r--r-- 1 500 500    4256 Mar 10 10:30 targets.sbml

====  ALLGO JOB SUCCESS  ====

10/03/2020 : Version 1.0, initial version

How to use our REST API :

Think to check your private token in your account first. You can find more detail in our documentation tab.

This app id is : 209

This curl command will create a job, and return your job url, and also the average execution time

files and/or dataset are optionnal, think to remove them if not wanted
curl -H 'Authorization: Token token=<your_private_token>' -X POST
-F job[webapp_id]=209
-F job[param]=""
-F job[queue]=standard
-F files[0]=@test.txt
-F files[1]=@test2.csv
-F job[file_url]=<my_file_url>
-F job[dataset]=<my_dataset_name> https://allgo.inria.fr/api/v1/jobs

Then, check your job to get the url files with :

curl -H 'Authorization: Token token=<your_private_token>' -X GET https://allgo.inria.fr/api/v1/jobs/<job_id>